geom_analysis.py

import numpy
import os

def calculate_distance(coords1, coords2):
    x_distance = coords1[0] - coords2[0]
    y_distance = coords1[1] - coords2[1]
    z_distance = coords1[2] - coords2[2]
    distance = numpy.sqrt(x_distance**2 + y_distance**2 + z_distance**2)
    return distance

def bond_check(bond_length, min_length=0, max_length=1.5):
    """
    Checks a bond distance to see if it meets the criteria for a bond based on a minimum and maximum length.
    The default minimum is 0 angstroms.  The default maximum is 1.5 angtroms.
    """
    if bond_length > min_length and bond_length < max_length:
        return True
    else:
        return False
    
def open_xyz(filename):
    """
    This function parses an xyz file and seperates the symbols and the coordinates.
    """
    xyz_file = numpy.genfromtxt(fname=filename, skip_header=2, dtype='unicode')
    symbols = xyz_file[:,0]
    coords = xyz_file[:,1:]
    coords = coords.astype(float) 
    return symbols, coords

file_location = os.path.join('data', 'water.xyz')
symbols, coordinates = open_xyz(file_location)
num_atoms = len(symbols)
for num1 in range(0, num_atoms):
    for num2 in range(0, num_atoms):
        if num1<num2:
            distance = calculate_distance(coordinates[num1], coordinates[num2])
            if bond_check(distance) is True:
                print(F'{symbols[num1]} to {symbols[num2]} : {distance:.3f}')